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brats_mri_segmentation

monai
medical
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katielink commited on
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ef9db36
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1 Parent(s): 9daa8eb

added train/val graphs

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Files changed (3) hide show
  1. README.md +11 -0
  2. configs/metadata.json +2 -1
  3. docs/README.md +11 -0
README.md CHANGED
@@ -15,6 +15,8 @@ The model is trained to segment 3 nested subregions of primary brain tumors (gli
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  - The TC describes the bulk of the tumor, which is what is typically resected. The TC entails the ET, as well as the necrotic (fluid-filled) and the non-enhancing (solid) parts of the tumor.
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  - The WT describes the complete extent of the disease, as it entails the TC and the peritumoral edema (ED), which is typically depicted by hyper-intense signal in FLAIR.
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  ## Data
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  The training data is from the [Multimodal Brain Tumor Segmentation Challenge (BraTS) 2018](https://www.med.upenn.edu/cbica/sbia/brats2018/tasks.html).
@@ -97,6 +99,15 @@ Execute inference:
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  python -m monai.bundle run evaluating --meta_file configs/metadata.json --config_file configs/inference.json --logging_file configs/logging.conf
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  ```
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  # Disclaimer
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  This is an example, not to be used for diagnostic purposes.
 
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  - The TC describes the bulk of the tumor, which is what is typically resected. The TC entails the ET, as well as the necrotic (fluid-filled) and the non-enhancing (solid) parts of the tumor.
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  - The WT describes the complete extent of the disease, as it entails the TC and the peritumoral edema (ED), which is typically depicted by hyper-intense signal in FLAIR.
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+ ![](https://developer.download.nvidia.com/assets/Clara/Images/clara_pt_brain_mri_segmentation_workflow.png)
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+
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  ## Data
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  The training data is from the [Multimodal Brain Tumor Segmentation Challenge (BraTS) 2018](https://www.med.upenn.edu/cbica/sbia/brats2018/tasks.html).
 
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  python -m monai.bundle run evaluating --meta_file configs/metadata.json --config_file configs/inference.json --logging_file configs/logging.conf
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  ```
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+ # Training
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+ A graph showing the training loss and the mean dice over 300 epochs.
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+ ![](https://developer.download.nvidia.com/assets/Clara/Images/monai_brats_mri_segmentation_train.png)
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+
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+ # Validation
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+ A graph showing the validation mean dice over 300 epochs.
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+ ![](https://developer.download.nvidia.com/assets/Clara/Images/monai_brats_mri_segmentation_val.png)
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+
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+
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  # Disclaimer
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  This is an example, not to be used for diagnostic purposes.
configs/metadata.json CHANGED
@@ -1,7 +1,8 @@
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  {
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  "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
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- "version": "0.3.5",
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  "changelog": {
 
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  "0.3.5": "update prepare datalist function",
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  "0.3.4": "update output format of inference",
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  "0.3.3": "update to use monai 1.0.1",
 
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  {
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  "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
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+ "version": "0.3.6",
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  "changelog": {
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+ "0.3.6": "added train/val graphs",
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  "0.3.5": "update prepare datalist function",
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  "0.3.4": "update output format of inference",
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  "0.3.3": "update to use monai 1.0.1",
docs/README.md CHANGED
@@ -8,6 +8,8 @@ The model is trained to segment 3 nested subregions of primary brain tumors (gli
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  - The TC describes the bulk of the tumor, which is what is typically resected. The TC entails the ET, as well as the necrotic (fluid-filled) and the non-enhancing (solid) parts of the tumor.
9
  - The WT describes the complete extent of the disease, as it entails the TC and the peritumoral edema (ED), which is typically depicted by hyper-intense signal in FLAIR.
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  ## Data
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  The training data is from the [Multimodal Brain Tumor Segmentation Challenge (BraTS) 2018](https://www.med.upenn.edu/cbica/sbia/brats2018/tasks.html).
@@ -90,6 +92,15 @@ Execute inference:
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  python -m monai.bundle run evaluating --meta_file configs/metadata.json --config_file configs/inference.json --logging_file configs/logging.conf
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  ```
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  # Disclaimer
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  This is an example, not to be used for diagnostic purposes.
 
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  - The TC describes the bulk of the tumor, which is what is typically resected. The TC entails the ET, as well as the necrotic (fluid-filled) and the non-enhancing (solid) parts of the tumor.
9
  - The WT describes the complete extent of the disease, as it entails the TC and the peritumoral edema (ED), which is typically depicted by hyper-intense signal in FLAIR.
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+ ![](https://developer.download.nvidia.com/assets/Clara/Images/clara_pt_brain_mri_segmentation_workflow.png)
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+
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  ## Data
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  The training data is from the [Multimodal Brain Tumor Segmentation Challenge (BraTS) 2018](https://www.med.upenn.edu/cbica/sbia/brats2018/tasks.html).
 
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  python -m monai.bundle run evaluating --meta_file configs/metadata.json --config_file configs/inference.json --logging_file configs/logging.conf
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  ```
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+ # Training
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+ A graph showing the training loss and the mean dice over 300 epochs.
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+ ![](https://developer.download.nvidia.com/assets/Clara/Images/monai_brats_mri_segmentation_train.png)
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+
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+ # Validation
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+ A graph showing the validation mean dice over 300 epochs.
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+ ![](https://developer.download.nvidia.com/assets/Clara/Images/monai_brats_mri_segmentation_val.png)
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+
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+
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  # Disclaimer
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  This is an example, not to be used for diagnostic purposes.